I'm not sure when it corrected itself, but my issue of not being able to see the options on the bottom seems to have been fixed. I know for a while it seemed that evernote was updating every time I logged on the computer for a few weeks back when I originally posted this issue. It hasn't auto-updated in a while. So maybe they fixed the issue!
The only option I see when clicking the 3 dots in the top-right is Quit Evernote, but since the other options are now appearing on the bottom of the UI like I was previously used to, I assume this is correct.
Running Big Sur and these screenshots were from an iMac Pro 27"